Abstract

There has been considerable effort to understand the inherent time scale for conformational reconfiguration of denatured proteins. Even a simple homopolymer, however, exhibits a spectrum of fluctuation time scales rather than a unique characteristic time. Consequently, different time scales may be probed by different measurements. Motivated by recent single-molecule fluorescence resonance energy transfer experiments, here I have studied theoretically how the characteristic time scale exhibited by fluctuations of the distance between two residues within an unfolded polypeptide depends on the choice of the residue pair. This time scale was generally found to become shorter as the sequence separation between the residues is reduced. The maximum reconfiguration time, however, corresponds not to the residues being located at the ends of the chain but rather to each residue residing a short length apart from the ends. Comparison of these findings with recent single-molecule measurements suggests that the latter may bear signatures of transient residual structure.

This work was supported by Grant No. CHE-0347862 from the NSF and Grant No. F-1514 from the Robert A. Welch Foundation. The CPU time was provided by the Texas Advanced Computing Center. I am grateful to Lei Huang for allowing me to use his code and to Ronald Levy and Ben Schuler for stimulating discussions.

Article outline:I. INTRODUCTIONII. MONOMER-DEPENDENT RECONFIGURATION TIME FOR A ROUSE CHAINA. Definition of reconfiguration timeB. Reconfiguration time decreases as the sequence separation between monomers is decreasedC. Reconfiguration time increases with increasing tail lengthIII. A MORE REALISTIC MODEL: FRET DYNAMICS IN AN UNFOLDED POLYPEPTIDEIV. DISCUSSIONA. Effects introduced by bulky dyesB. Internal friction effectsC. Effect of residual order